Specialized substrates are injected into a host cell through secretion system, to destroy various signal pathways, which is an effective way for bacterial colonization and infection. Vibrio parahaemolyticus being an important foodborne pathogen, its Type Ⅲ Secretion System (T3SS) and Type VI Secretion System (T6SS) are important virulence factors to the hosts. In this review, we summarize the specific roles of T3SS and T6SS effectors in pathogenicity and the related regulatory mechanisms. This paper provides a reference to further understand the diseases caused by Vibrio parahaemolyticus, to investigate its pathogenesis and find the pathogenic targets.